In 1919, Cawthon took his first regular coaching job at Beaumont High School before becoming the baseball and basketball coach at Rice Institute—now Rice University—in 1920. In 1923 he moved on to coach at Austin College in Sherman, Texas, where he established the Cawthon Trophy, given annually to an outstanding individual at the school on the basis of athletic participation, leadership, and sportsmanship. His record at Austin College was 21–20–4 from 1923 to 1927. Austin won Texas Intercollegiate Athletic Association title in 1923.
In 1930, Cawthon was hired by Texas Technological College—now Texas Tech University. By 1932, the Matadors—now the Red Raiders)—became the highest-scoring team in the nation. He coached at the school through the 1940 season. During his tenure, he compiled a record of 76–32–6.